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Publications

Selected Publications

  • Liou, J.S.-C. B. Szostek, C.M. DeRito, and E.L. Madsen. 2010. Investigating the biodegradability of perfluorooctanoic acid. Chemosphere 79: (in press)
  • Madsen, E.L. 2010. Stable Isotope probing techniques and bioremediation, pp . IN Stable isotope probing in microbial molecular ecology. J.C. Murrel and A. Whiteley (eds). American Society for Microbiology Press. Washington DC (in press)
  • Yagi, J.M., C.M. DeRito, J.M. Suflita, L. Geig, C.-O. Jeon, and E.L. Madsen. 2010. Subsurface microbial communities involved in in situ naphthalene catabolism carry out a complete N cycle via dissimilatory nitrate reduction to ammonia and nitrification. Appl. Environ Microbiol 76:3124-3134.
  • Yagi. J.M., D. Sims, T. Brettin, D. Bruce and E.L. Madsen. 2009. Remarkable physiologival versatility revealed by whole-genome analysis of the aromatic-hydrocarbon-degrading bacterium, Polaromonas naphthalenivorans. Environ Microbiol 11:2253-2270.
  • Yagi J.M., E.F. Neuhauser, J. Ripp, D. Mauro and E. L. Madsen. 2009. Subsurface ecosystem resilience: Long-term attenuation of subsurface contaminants supports an elaborate eukaryotic food chain and a dynamic microbial community. ISME Journal 4:131-143.
  • Madsen, E.L. 2009. Exclude "unculturable" from the taxonomic microbiology literature (Letter to Editor). Microbe 4:351.
  • Yagi, J.M. and E.L. Madsen. 2009. Diversity and spatial/temporal variability of oxygenase genes and nah/nag mRNA transcripts in a shallow contaminated aquifer. Appl Environ Microbiol 75:6478-6487.
  • DeRito, C.M. and E.L. Madsen. 2009. Stable isotope probing reveals Trichosporon yeast to be active in situ in soil phenol metabolism. ISME Journal ISME Journal 3:477-485.
  • Pumphrey, G.M., B.T. Hanson, S. Chandra, and E.L. Madsen. 2009. Dynamic secondary ion mass spectrometry (SIMS) imaging of microbial populations utilizing 13C-labeled substrates in pure culture and in soil. Environ. Microbiol. 11:220-229.
  • Madsen, E.L. 2008. Environmental Microbiology: From Genomes to Biogeochemistry. Wiley Blackwell. Malden MA, 479 pp.
  • Kim, J.M., N.T. Le, B.S. Chung, J.H. Park, J.-W. Bae, E.L. Madsen, and C.-O. Jeon. 2008. Influence of soil components on the biodegradation of benzene, toluene, ethbenzene, and o-, m-, and p-xylenes by the newly isolated bacterium Pseudoxanthomonas spadix BD-a59. Appl. Environ. Microbiol. 74:7313-7320.
  • Chandra, S., G.M. Pumphrey, J.M. Abraham, and E.L. Madsen. 2008. Dynamic SIMS ion microscopy imaging of individual bacterial cells for studies of isotopically labeled molecules. Appl. Surface Sci. 255:847-851.
  • Pumphrey, G.M. and E.L. Madsen. 2008. Field-based stable isotope probing reveals the identities of benzoic acid-metabolizing microorganism and their in situ growth in agricultural soil. Appl. Environ. Microbiol. 74:4111-4118.
  • J.S-C. Liou, C.M. DeRito, and E.L. Madsen. 2008. Field-based and laboratory stable isotope probing surveys of the identities of both aerobic and anaerobic benzene-metablolizing microorganisms in freshwater sediment. Environ. Microbiol. 10:1964-1977.
  • Liou, J. and E.L. Madsen. 2008. Microbioal ecological processrs: Aerobic/Anaerobic. IN Encyclopedia of Ecology (S.E. Jorgensen ed.) Elsevier Science Ltd. Oxford UK.
  • Pumphrey, G.M. and E.L.Madsen 2007. Naphthalene metabolism and growth inhibition by naphthalene in Polaraomonas naphthlenivorans strain CJ2. Microbiology 153:3739-3747.
  • Park, M., Y. Jeon, Y., H.-S. Ro., W. Park, E. L. Madsen and C.- O. Jeon. 2007. Molecular and Biochemical Characterization of 3-Hydroxybenzoate 6-hydroxylase from Polaromonas naphthalenivorans CJ2. Appl. Environ. Microbiol. 73: 5146-5152.
  • Kang, Y.-S., Y. Lee, H. Jung, C.-O. Jeon, E. L. Madsen, and W. Park. 2007. Overexpressing antioxidant enzymes enhances naphthalene biodegradation in Pseudomonas sp. Strain As1. Microbiology. 153:3246-3254.
  • Madsen. E.L. 2006. The use of stable isotope probing techniques in bioreactor and field studies on bioremediation. Curr. Opin. Biotechnol. 17: 92-97.
  • Lee, Y.,E. Ahn, S.Park, E.L.Madsen, C. Jeon, and W. Park. 2006. Construction of a reporter strain Pseudomonas putida for the detection of oxidative stress caused by environmental pollutants. J. Microrbiol. Biotechnol. 16: 386-390.
  • Jeon , C.-O, M. Park, H.-S. Rob, W. Park, and E. L. Madsen. 2006. The naphthalene catabolic (nag) genes of Polaromonas naphthalenivoransCJ2: Evolutionary implications for two gene clusters and novel regulatory control. Appl. Environ. Microbiol. 72: 1086-1095.
  • Madsen, E. L. 2005. Identifying microorganisms responsible for ecologically significant biogeochemical processes. Nature Reviews Microbiology 3:439-446.
  • Park, W. and E. L. Madsen. 2004. Characterization of nah in Pseudomonas putida Cg1 and its role in bacterial survival in soil. Appl. Microbiol. Biotechnol. 66:209-216.
  • Jeon, C.-O., W. Park, W. C. Ghiorse, and E. L. Madsen. 2004. Polaromonas naphthalenivorans gen. nov., sp. nov., a naphthalene -degrading bacterium from naphthalene-contaminated sediment. Intl. J. Syst. Evol. Microbiol. 54:93-97.
  • Weiss, J. M., A. J. McKay, C. DeRito, C. Watanabe, K. A. Thorn, and E. L. Madsen. 2004. Development and application of pyrolysis-gas chromatography/mass spectrometry for the analysis of bound trinitrotoluene residues in soil. Environ. Sci. Technol. 38:2167-2174.
  • Park, W., C.-O. Jeon, H. Cadillo, C. DeRito, and E. L. Madsen. 2004. Survival of naphthalene-degrading Pseudomonas putida NCIB 9816-04 in naphthalene-amended soil: Toxicity of naphthalene and its metabolites. Appl. Microbiol. Biotechnol. 64:429-435.
  • Miller, D. N., J. B. Yavitt, E. L. Madsen, and W. C. Ghiorse. 2004. Methanotrophic activity, abundance, and diversity in forest swamp pools: spatiotemporal dynamics and influences on methane fluxes. Geomicrobiol. J. 21:257-271.
  • Jeon, C.-O., W. Park, P. Padmanabhan, C. DeRito, J. R. Snape, and E. L. Madsen. 2003. Discovery of a novel bacterium with distinctive dioxygenase that is responsible for in situ biodegradation in a contaminated sediment. Proc. Natl. Acad. Sci. USA 100:13591-13596.
  • Park, W., C.-O. Jeon, A. M. Hohnstock-Ashe, S. C. Winans, B. J. Zylstra, and E. L. Madsen. 2003. Identification and characterization of the conjugal transfer region of the pCg1 plasmid from naphthalene-degrading Pseudomonas putida Cg1. Appl. Environ. Microbiol. 69:3263-3271.
  • Wilson, M. S., J. B. Herrick, C. O Jeon, D. E. Hinman, and E. L. Madsen. 2003. Horizontal transfer of phn-Ac dioxygenase genes within one of two phenotypically and genotypically distinctive naphthalene-degrading guilds from adjacent soil environments. Appl. Environ. Microbiol. 69:2172-2181.
  • Padmanabhan, P., S. Padmanabhan, C. DeRito, A. Gray, D. Gannon, J. R. Snape, C.S. Tsai, W. Park, C. Jeon, and E. L. Madsen. 2003. Respiration of 13C-labeled substrate added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA. Appl. Environ. Microbiol. 69:1614-1622.
  • Park, W., C.-O. Jeon, and E. L. Madsen. 2002. Interaction of NahR, a LysR-type transcriptional regulator, with the alpha subunit of RNA polymerase in the naphthalene degrading bacterium, Pseudomonas putida NCIB 9816-4. FEMS Microbiol. Lett 213:159-165.
  • Park, W., P. Padmanabhan, S. Padmanabhan, G. J. Zylstra, and E. L. Madsen. 2002. nahR, encoding a LysR-type transcriptional activator, is highly conserved among naphthalene degrading bacteria isolated from a coal tar waste-contaminated site and in extracted community DNA. Microbiol. 148:2319-2329.
  • Bakermans, C. and E. L. Madsen. 2002. Detection in coal tar waste-contaminated groundwater of mRNA transcripts related to naphthalene dioxygenase by fluorescent in situ hybridization (FISH) with tyramide signal amplification (TSA). J. Microbiol. Meth. 50:75-84.
  • Bakermans, C., A. M. Hohnstock-Ashe, S. Padmanabhan, P. Padmanabhan, and E. L. Madsen. 2002. Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar wastes by subsurface microorganisms. Microb. Ecol. 44:107-117.
  • Bakermans, C. and E. L. Madsen. 2002. Diversity of 16S rRNA as naphthalene dioxygenase genes from a coal tar waste-contaminated aquifer waters. Microb. Ecol. 44:95-106.
  • Madsen, E. 2002. Methods for Assessing Biodegradability: Field and Laboratory, pp. 475-484. In: G. Bitton (Ed.) Encyclopedia of Environmental Microbiology. Wiley, New York, NY.
  • Madsen, E.L. 2002. Methods for determining biodegradability, pp. 903-913. In: C. J. Hurst, et al. (ed.). Manual of Environmental Microbiology, 2nd ed. ASM, Washington, DC.
  • Madsen, E. 2002. Horizontal transfer of naphthalene catabolic genes in a contaminated aquifer, pp. 35-42. In: M. Syvanen and C. I. Kato (Eds.)Horizontal Gene Transfer, 2nd ed. Chapman and Hall, New York, NY.
  • Lowe, M., F. Robb, E. L. Madsen, and R. Halden. 2002. Geochemistry and microbial diversity of a trichloroethene-contaminated superfund site undergoing intrinsic in situ reductive dechlorination. FEMS Microbial Ecol. 40:123-134.
  • Hohnstock-Ashe, A. M., Plummer, S. M., R. M. Yager, P. Baveye, and E. L. Madsen. 2001. Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: Geochemical and microbial controls on in situ reductive dechlorination. Environ. Sci. Technol.35:4449-4456.
  • Madsen, E.L. 2001. Natural Attenuation of Organic Contaminants, pp. 249-278. In: J. K. Fredrickson and M. Fletcher (ed.) Subsurface Microbiology and Biogeochemistry. John Wiley and Sons, NY.
  • Bakermans, C. and E. L. Madsen. 2000. Use of substrate responsive direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community. J. Microbiol. Meth. 43:81-90.
  • National Research Council. 2000. Natural attenuation for groundwater remediation. National Academic Press. Washington, DC.
  • Hohnstock, A. M., K. G. Stuart-Keil, E. E. Kull, and E. L. Madsen. 2000. Naphthalene and donor cell density influence field conjugation of naphthalene catabolic plasmids. Appl. Environ. Microbiol. 66:3088-3092. Miller, D. N., J. E. Bryant, E. L. Madsen, and W. C. Ghiorse. 1999. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples. Appl. Environ. Microbiol. 65:4715-4724.
  • Kalogeraki, V., J. Zhu, A. Eberhard, E. L. Madsen, and S. C. Winans. 1999. The phenolic vir gene inducer ferulic acid is O-demethylated by the VirH2 protein of an Agrobacterium tumefaciens Ti plasmid. Molec. Microbiol. 34:512-522.
  • Wilson, M.S., C. Bakermans, and E. L. Madsen. 1999. In situ, real-time catabolic gene expression: Extraction and characterization of naphthalene dioxygenase mRNA transcripts from groundwater. Appl. Environ. Microbiol. 65:80-87.
  • Madsen, E. L. 1998. Theoretical and Applied Aspects of Bioremediation: The Influence of Microbiological Processes on Organic Compounds in Field Sites, pp. 354-407. In: R. Burlage, R. Atlas, D. Stahl, G. Geesey, G. Sayler (eds.)Techniques in Microbial Ecology. Oxford University Press. New York, NY.
  • Stuart-Keil, K.G., A.M. Hohnstock, K.P. Drees, J.B. Herrick. and E. L. Madsen. 1998. Plasmids responsible for horizontal transfer of naphthalene catabolic genes between bacteria at a coal tar-contaminated site are homologous to pDTG1 from Pseudomonas putida 9816-4. Appl. Environ. Microbiol. 64: 3633-3640.
  • Madsen, E. L. 1998. Epistemology of environmental microbiology. Environ. Sci. Technol. 32: 429-539.
  • Madsen, E. L. 1997. Themes and variations of aromatic hydrocarbon catabolism by microorganisms in a contaminated field site. In: Progress in Microbial Ecology. Proceedings of the 7th International Symposium on Microbial Ecology. M. T. Martins et al., (eds).pp. 587-596.
  • Yager, R. M., S. E. Bilotta, C. L. Mann, and E. L. Madsen. 1997. Metabolic adaptation and In situ attenuation of chlorinated ethenes by naturally-occurring microorganisms in a fractured dolomite aquifer near Niagara Falls, NY. Environ. Sci. Technol. 31:3138-3147.
  • Herrick, J. B., K. G. Stuart-Keil, W. C. Ghiorse, and E. L. Madsen. 1997. Natural horizontal transfer of a naphthalene dioxygenase gene between bacteria native a contaminated field site. Appl. Environ. Microbiol. 63:2330-2337.
  • Herrick, J. B., D. N. Miller, E. L. Madsen, and W. C. Ghiorse. 1997. Extraction, purification, and PCR amplification of microbial DNA from sediments and soils. In: J. Burke (ed.) PCR: Essential Techniques. Bios Scientific Publishers, Oxford.
  • Williams, R. A., K. A. Shuttle, J. L. Kunkler, E. L. Madsen, and S. W. Hooper. 1997. Intrinsic bioremediation in a solvent - contaminated alluvium. J. Ind. Microbiol. Biotechnol. 18:177-188.
  • Madsen, E. L. 1997. Methods for determining biodegradability. In: C. J. Hurst, et al. (ed.). Manual of Environmental Microbiology. American Society for Microbiology, Washington, DC, pp. 709-720.
  • Sandoli, R. S., W. C. Ghiorse, and E. L. Madsen. 1996. Regulation of microbial phenanthrene mineralization in sediments by sorbent- sorbate contact time, inoculum, and gamma irradiation-induced sterilization artifacts. Environ. Toxicol. Chem.15:1901-1907.
  • Madsen, E. L., C. L. Mann, and S. Bilotta. 1996. Oxygen limitations and aging as explanation for the persistence of naphthalene in coal-tar contaminated surface sediments. Environ. Toxicol. Chem. 15:1876-1882.
  • Madsen, E. L., C. T. Thomas, M. S. Wilson, R. L. Sandoli, and S. B. Best. 1996. In situ dynamics of aromatic hydrocarbons (AHs) and bacteria capable of AH metabolism in a coal tar waste-contaminated field site. Environ. Sci. Technol. 30:2412-2416.
  • Madsen, E. L. 1996. Hydrogen-based microbial ecosystems - a clarification. Technical comment Science (272:896).
  • Madsen, E. L. 1996. A critical analysis of methods for determining the composition and biogeochemical activities of soil microbial communities in situ. In: G. Stotzky and J.-M. Bollag (eds.). Soil Biochemistry, Vol. 9:287-370.
  • Wilson, M. S., and E. L. Madsen. 1996. Field extraction of a unique intermediary metabolite indicative of real time In situ pollutant biodegradation. Environ. Sci. Technol. 30:2099-2103.
  • Ghiorse, W. C., J. B. Herrick, R. L. Sandoli, and E. L. Madsen. 1995. Natural selection of PAH-degrading bacterial guilds at coal tar disposal sites. Environmental Health Perspectives 103(5):107-111.
  • Madsen, E. L. 1995. Impacts of agricultural practices on subsurface microbial ecology. In: D. Sparks (ed.). Advances in Agronomy Vol. 54, pp. 1-67.
  • Madsen, E. L., S. E. Bilotta-Best, and W. C. Ghiorse. 1995. Development of a rapid 14C-based field method for assessing potential biodegradation of organic compounds in soil and sediment samples. J. Microbiol. Meth. 21:317-327.
  • Moré, M. I., J. B. Herrick, M. C. Silva, W. C. Ghiorse, and E. L. Madsen. 1994. Quantitative cell lysis of indigenous microorganisms and rapid extraction of microbial DNA from sediment. Appl. Environ. Microbiol. 60:1572-1580.
  • National Research Council. 1993. In situ Bioremediation: When Does It Work? B. E. Rittmann, J. M. Tiedje, R. Brown (Executive Committee); E. L. Madsen (Rapporteur). National Academy Press, Washington, DC.
  • Madsen, E. L. and W. C. Ghiorse. 1993. Ground Water Microbiology: Subsurface ecosystem processes. pp. 167-213. In: Ford, T. (ed.) Aquatic Microbiology: An Ecological Approach. Blackwell Scientific Publications, Cambridge, MA.
  • Herrick, J. B., E. L. Madsen, C. A. Batt, and W. C. Ghiorse. 1993. Polymerase chain reaction amplification of naphthalene catabolic and 16S rRNA gene sequences from indigenous sediment bacteria. Appl. Environ. Microbiol. 59:687-694.
  • Madsen, E. L., A. Winding, K. Malachowsky, C. T. Thomas, and W. C. Ghiorse. 1992. Contrasts between subsurface microbial communities and their metabolic adaptation to polycyclic aromatic hydrocarbons at a forested and urban coal tar disposal site. Microb. Ecol. 24:199-213.
  • Madsen, E. L. 1991. Determining in situ biodegradation: Facts and challenges. Environ. Sci. Technol. 25:1662-1673.
  • Madsen, E. L., J. L. Sinclair and W. C. Ghiorse. 1991. In situ biodegradation: Microbiological patterns in a contaminated aquifer. Science 252:830-833.
  • Madsen, E. L. and J.-M. Bollag. 1989. Pathway of indole metabolism by a denitrifying microbial community. Arch. Microbiol. 151:71-76.
  • Madsen, E. L. and J.-M. Bollag. 1989. Aerobic and anaerobic microbial activity in deep subsurface sediments from the Savannah River Plant. Geomicrobiol. J. 7:93-102.
  • Madsen, E. L., A. J. Francis, and J.-M. Bollag. 1988. Environmental factors affecting indole metabolism under anaerobic conditions. Appl. Environ. Microbiol. 54:74-78.
  • Berry, D. F., E. L. Madsen, and J.-M. Bollag. 1987. Conversion of indole to oxindole under methanogenic conditions. Appl. Environ. Microbiol. 53:180-182.
  • Madsen, E. L., M. D. Morgan, and. R. E. Good. 1986. Simultaneous photoreduction and microbial oxidation of iron in a stream in the New Jersey Pinelands. Limnol. Oceanogr. 31:832-838.
  • Madsen, E. L. and M. Alexander. 1985. Effects of chemical speciation on the mineralization of organic compounds by microorganisms. Appl. Environ. Microbiol. 50:342-349.
  • Wang, Y. S., E. L. Madsen, and M. Alexander. 1985. Microbial degradation by mineralization or cometabolism determined by chemical concentration and environment. J. Ag. Food Chem. 33:495-499.
  • Madsen, E. L. and M. Alexander. 1982. Transport of Rhizobium and Pseudomonas through soil. Soil Sci. Soc. Am. J. 46:557-560.